Contacts of the strand formed by residues 215 - 222 (chain I) in PDB entry 6RAR
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 215 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175I THR 3.8 0.9 - - - +
176I ILE* 3.7 2.3 - - - +
177I ILE* 2.8 47.0 + - + +
211I ALA* 5.4 4.7 - - + -
213I TYR 3.7 9.0 - - - +
214I ASP* 1.3 74.5 - - - +
216I VAL* 1.3 71.4 + - - +
217I LEU* 3.9 23.8 - - + -
251I LEU* 4.4 15.9 - - + -
252I CYS 3.5 26.9 - - - +
253I PRO* 4.1 7.0 - - + -
254I LEU* 4.0 1.9 - - - +
262I TRP* 6.3 0.4 - - + -
276I TRP* 3.9 25.4 - - + +
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Residues in contact with VAL 216 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174I LEU* 4.0 33.0 - - + -
175I THR 3.5 7.9 - - - +
176I ILE* 4.2 11.2 - - + -
215I LEU* 1.3 76.6 - - - +
217I LEU* 1.3 67.1 + - - +
218I ASP* 4.1 0.6 + - + +
251I LEU* 3.2 6.8 - - - +
252I CYS* 2.6 47.6 + - + +
254I LEU* 3.6 31.2 - - + -
257I PHE* 4.0 27.4 - - + -
330I TYR* 5.1 2.5 - - - +
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Residues in contact with LEU 217 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173I VAL 3.9 1.2 - - - +
174I LEU* 3.6 2.1 - - - -
175I THR* 2.8 56.3 + - + +
177I ILE* 4.0 23.6 - - + -
202I ILE* 4.9 6.3 - - + -
215I LEU* 3.9 25.4 - - + -
216I VAL* 1.3 74.4 - - - +
218I ASP* 1.3 61.5 + - - +
219I GLY 4.1 0.2 + - - -
246I LEU* 6.0 0.4 - - + -
248I LEU* 3.7 30.3 - - + +
250I ASP 3.8 1.8 - - - +
251I LEU* 4.1 15.3 - - + -
273I VAL* 4.7 5.8 - - + -
276I TRP* 4.1 33.4 - - + -
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Residues in contact with ASP 218 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172I ARG* 2.6 48.8 + - - -
173I VAL 3.8 5.1 - - - +
174I LEU* 3.8 10.8 - - + +
216I VAL* 4.1 1.1 - - + -
217I LEU* 1.3 71.9 - - - +
219I GLY* 1.3 65.2 + - - +
248I LEU* 3.5 4.4 - - - -
249I PHE* 2.9 31.3 + - - -
250I ASP* 2.9 30.0 + - + +
251I LEU* 4.6 0.9 - - - +
330I TYR* 2.8 30.8 + - - +
338I TRP* 4.0 3.1 - - - -
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Residues in contact with GLY 219 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172I ARG* 3.7 10.0 - - - -
173I VAL 2.9 33.2 + - - +
217I LEU 4.1 0.4 + - - -
218I ASP* 1.3 80.0 + - - +
220I GLU* 1.3 58.1 + - - -
246I LEU* 4.2 4.7 - - - -
247I HIS 3.2 13.5 - - - -
248I LEU* 3.9 8.4 - - - +
249I PHE* 3.3 13.0 - - - -
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Residues in contact with GLU 220 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C C 5.3 0.3 - - - +
101C MN 3.9 3.8 + - - -
300D AMP 2.2 48.3 + - + -
168I LEU* 3.4 25.4 - - + +
170I GLY* 2.9 42.1 + - - +
171I VAL* 3.5 15.4 - - - -
172I ARG* 3.6 1.7 + - - -
219I GLY* 1.3 74.0 - - - +
221I VAL* 1.3 61.0 + - - +
222I MET* 4.1 1.1 - - + +
246I LEU* 4.0 1.3 - - - -
247I HIS* 2.8 41.6 + - - +
249I PHE* 3.3 11.6 - - + -
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Residues in contact with VAL 221 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170I GLY* 3.4 4.0 - - - -
171I VAL* 3.1 37.5 + - + +
173I VAL* 3.3 28.4 - - + +
184I MET* 6.5 0.2 - - + -
195I PHE* 3.9 27.6 - - + -
198I ILE* 4.5 5.8 - - + -
220I GLU* 1.3 71.7 - - - +
222I MET* 1.3 62.9 + - - +
229I LEU* 3.3 11.4 - - + +
244I ALA* 3.7 27.6 - - + -
245I VAL 3.4 11.9 - - - +
246I LEU* 4.1 9.6 - - + +
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Residues in contact with MET 222 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168I LEU* 3.5 24.7 - - + -
169I ASP* 3.1 51.6 - - + +
170I GLY 3.5 2.2 - - - -
220I GLU* 4.1 4.9 - - + +
221I VAL* 1.3 79.0 - - - +
223I SER* 1.3 72.7 + - - +
225I ASN* 5.9 3.6 - - - -
229I LEU* 4.4 7.0 - - - -
243I ASP 4.7 0.2 - - - +
244I ALA* 3.4 5.2 - - - -
245I VAL* 2.9 32.0 + - + +
247I HIS* 3.9 28.5 - - + +
318I TYR* 5.8 5.2 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il